Chapter 9 Differential abundance analysis: functional

9.1 Wilcoxon

9.1.1 Community elements differences:

   Elements         high          low                                        Function
1     B0205 5.545938e-01 6.265510e-01               Amino acid biosynthesis_Threonine
2     B0208 6.271503e-01 7.060346e-01                  Amino acid biosynthesis_Valine
3     B0210 6.016381e-01 6.799657e-01                 Amino acid biosynthesis_Leucine
4     B0211 7.208532e-01 7.845367e-01                  Amino acid biosynthesis_Lysine
5     B0212 5.374306e-01 6.135838e-01                Amino acid biosynthesis_Arginine
6     B0216 4.008679e-01 5.191861e-01              Amino acid biosynthesis_Tryptophan
7     B0217 3.860860e-01 4.488773e-01           Amino acid biosynthesis_Phenylalanine
8     B0218 3.110587e-01 3.672414e-01                Amino acid biosynthesis_Tyrosine
9     B0302 1.313611e-02 2.632273e-02      Amino acid derivative biosynthesis_Betaine
10    B0303 2.125935e-01 2.488038e-01      Amino acid derivative biosynthesis_Ectoine
11    B0309 7.951187e-02 9.738120e-02   Amino acid derivative biosynthesis_Putrescine
12    B0310 2.022088e-03 6.875040e-03   Amino acid derivative biosynthesis_Tryptamine
13    B0403 5.259044e-01 5.583029e-01                    SCFA biosynthesis_Propionate
14    B0602 7.454626e-01 7.952110e-01             Organic anion biosynthesis_Fumarate
15    B0710 6.864721e-02 1.197774e-01         Vitamin biosynthesis_Phylloquinone (K1)
16    B0804 7.219838e-01 7.756036e-01     Aromatic compound biosynthesis_Dipicolinate
17    B0805 1.637677e-01 2.235599e-01 Aromatic compound biosynthesis_Indole-3-acetate
18    B0902 3.727339e-03 1.408047e-02            Metallophore biosynthesis_Aerobactin
19    B1012 3.984627e-02 2.523846e-02              Antibiotic biosynthesis_Fosfomycin
20    B1014 2.069216e-03 3.070448e-04              Antibiotic biosynthesis_Kanosamine
21    B1028 1.148606e-02 2.245694e-02               Antibiotic biosynthesis_Pyocyanin
22    B1029 4.284736e-04 1.457010e-06            Antibiotic biosynthesis_Pyrrolnitrin
23    D0104 1.242776e-01 1.799243e-01            Lipid degradation_Dicarboxylic acids
24    D0204 4.119183e-01 4.724725e-01               Polysaccharide degradation_Chitin
25    D0206 4.753334e-01 5.678805e-01       Polysaccharide degradation_Alpha galactan
26    D0211 8.531451e-02 1.122141e-01         Polysaccharide degradation_Alpha-mannan
27    D0213 2.955001e-01 3.571304e-01                Polysaccharide degradation_Mucin
28    D0301 1.478514e-02 3.667093e-02                       Sugar degradation_Lactose
29    D0302 8.731257e-02 1.299471e-01                       Sugar degradation_Sucrose
30    D0310 3.788951e-01 4.599128e-01                         Sugar degradation_NeuAc
31    D0501 7.384596e-01 8.168574e-01                   Amino acid degradation_Serine
32    D0502 2.960380e-01 3.904288e-01                Amino acid degradation_Threonine
33    D0508 3.114233e-02 7.625305e-02                   Amino acid degradation_Lysine
34    D0603 6.322401e-03 1.820880e-02             Nitrogen compound degradation_Urate
35    D0604 5.681134e-01 6.013131e-01            Nitrogen compound degradation_GlcNAc
36    D0606 2.153605e-02 3.378014e-02         Nitrogen compound degradation_Allantoin
37    D0611 2.988320e-03 4.087332e-02  Nitrogen compound degradation_Phenylethylamine
38    D0701 9.514933e-03 1.967072e-02              Alcohol degradation_2,3-Butanediol
39    D0704 3.438279e-01 4.521028e-01                    Alcohol degradation_Glycerol
40    D0709 1.302359e-05 6.776383e-04           Alcohol degradation_Polyvinyl alcohol
41    D0805 1.015905e-02 2.782693e-02                 Xenobiotic degradation_Benzoate
42    D0807 3.385425e-02 6.491818e-02                 Xenobiotic degradation_Catechol
43    D0815 3.794043e-06 2.070123e-04                Xenobiotic degradation_Phthalate
44    D0816 9.785049e-02 1.448659e-01            Xenobiotic degradation_Phenylacetate
45    D0903 3.822127e-02 1.095909e-01            Antibiotic degradation_Cephalosporin
46    D0906 1.585863e-06 2.020556e-04               Antibiotic degradation_Fosfomycin
47    D0910 4.777951e-01 5.764713e-01          Antibiotic degradation_Chloramphenicol
48    S0104 2.074062e-01 2.355010e-01            Cellular structure_Lipoteichoic acid

9.1.2 Community functions differences

  Code_function       high       low                       Function
1           B02 0.52137130 0.5740600        Amino acid biosynthesis
2           B06 0.64729040 0.6917290     Organic anion biosynthesis
3           B08 0.41848200 0.4617373 Aromatic compound biosynthesis
4           D02 0.33806480 0.3876675     Polysaccharide degradation
5           D05 0.30239730 0.3394142         Amino acid degradation
6           D06 0.14482000 0.1610282  Nitrogen compound degradation
7           D08 0.01519399 0.0275254         Xenobiotic degradation
8           D09 0.18677310 0.2091800         Antibiotic degradation

9.1.3 Community domains differences

   Code_domain      high       low
1 Biosynthesis 0.3862795 0.4127321
2  Degradation 0.1945182 0.2257702

9.2 ANCOM-BC2

9.2.1 Without random effect

9.2.1.1 Element level

9.2.1.2 Functional level

  taxon lfc_environmentlow p_environmentlow      Domain               Function
1   D08          0.4125544     0.0001466292 Degradation Xenobiotic degradation

9.2.2 Witho random effect

9.2.2.1 Element level

   taxon lfc_environmentlow p_environmentlow       Domain                                        Function            Element
1  B1014         -2.7787038     3.099009e-08 Biosynthesis              Antibiotic biosynthesis_Kanosamine         Kanosamine
2  B0805          0.2127575     2.004379e-02 Biosynthesis Aromatic compound biosynthesis_Indole-3-acetate   Indole-3-acetate
3  D0104          0.2474646     1.314513e-02  Degradation            Lipid degradation_Dicarboxylic acids Dicarboxylic acids
4  D0302          0.2863871     8.446544e-03  Degradation                       Sugar degradation_Sucrose            Sucrose
5  B1028          0.4167257     1.612048e-02 Biosynthesis               Antibiotic biosynthesis_Pyocyanin          Pyocyanin
6  D0807          0.4763618     4.498157e-04  Degradation                 Xenobiotic degradation_Catechol           Catechol
7  D0508          0.5163037     2.604708e-02  Degradation                   Amino acid degradation_Lysine             Lysine
8  D0701          0.5375975     5.634684e-03  Degradation              Alcohol degradation_2,3-Butanediol     2,3-Butanediol
9  B0302          0.5436327     1.828069e-02 Biosynthesis      Amino acid derivative biosynthesis_Betaine            Betaine
10 D0301          0.5948345     1.646718e-02  Degradation                       Sugar degradation_Lactose            Lactose
11 B0902          0.6772208     3.927887e-02 Biosynthesis            Metallophore biosynthesis_Aerobactin         Aerobactin
12 D0805          0.6939341     6.786145e-03  Degradation                 Xenobiotic degradation_Benzoate           Benzoate
13 D0517          0.6984238     1.645718e-02  Degradation                Amino acid degradation_Ornithine          Ornithine
14 D0903          0.7583944     4.002996e-03  Degradation            Antibiotic degradation_Cephalosporin      Cephalosporin
15 D0603          0.8707816     1.547040e-03  Degradation             Nitrogen compound degradation_Urate              Urate
16 B0310          1.4653554     3.161436e-04 Biosynthesis   Amino acid derivative biosynthesis_Tryptamine         Tryptamine
17 D0709          1.8839060     1.386329e-02  Degradation           Alcohol degradation_Polyvinyl alcohol  Polyvinyl alcohol
18 D0815          1.9151895     1.405453e-02  Degradation                Xenobiotic degradation_Phthalate          Phthalate
19 D0806          1.9633790     1.324239e-02  Degradation             Xenobiotic degradation_Anthranilate       Anthranilate

9.2.2.2 Functional level

  taxon lfc_environmentlow p_environmentlow      Domain               Function
1   D08          0.4224442     0.0002953342 Degradation Xenobiotic degradation